frankie is getting a similar problem in maya 2008, although i don't know if it's tied to the selection method - whenever he selects something it takes 2-3 seconds to actually select it (with just the channel box/layer editor on the right, not the attribute editor). having the attribute editor open is a surefire way of…
try putting "MAYA_NO_VERTEX_ARRAY_SELECT = 1" in your maya.env file in my documents\maya\8.5 might have to create it, and i'm pretty sure doing that helped me with selection issues.